The pilot of a Transport is pretty much just responsible for pointing it the direction they want to go, the crew are the ones doing the interesting things. So that's why it makes sense to me.Well, considering we don't know a whole lot about how those ships works, that seems like a pretty premature statement.
That doesn't fit with the game mechanics though - it's the pilot's skill level that determines when you move and when you do actions, and that's as relevant to this ship as any other.
Funny thing is, a low pilot skill like 3 could actually be beneficial here - you can move before a lot of ships and potentially kill them in a collision, especially if they were ionised a couple of turns ago forcing them into your path. Players playing against a Transport and Y-Wing escort are going to have to be very careful where they put their ships!